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Journal of Bioinformatics and Computational Biology

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https://www.readbyqxmd.com/read/28201946/sorting-permutations-by-prefix-and-suffix-rearrangements
#1
Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias
Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations...
February 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178888/histone-modifications-influence-skipped-exons-inclusion
#2
Yue Hou, Huan Huang, Wenqiao Hu, Hongde Liu, Xiaosun
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons...
February 8, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28110602/sitex-2-0-projections-of-protein-functional-sites-on-eukaryotic-genes-extension-with-orthologous-genes
#3
Irina V Medvedeva, Pavel S Demenkov, Vladimir A Ivanisenko
Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem...
January 23, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28178889/v-elmpirnapred-identification-of-human-pirnas-by-the-voting-based-extreme-learning-machine-v-elm-with-a-new-hybrid-feature
#4
Cong Pian, Yuan-Yuan Chen, Jin Zhang, Zhi Chen, Guang-Le Zhang, Qiang Li, Tao Yang, Liang-Yun Zhang
Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this paper, we introduce a series of new features with 80 dimension called short sequence motifs (SSM). A hybrid feature vector with 1444 dimension can be formed by combining 1364 features of [Formula: see text]-mer strings and 80 features of SSM features. We optimize the 1444 dimension features using the feature score criterion (FSC) and list them in descending order according to the scores...
January 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28033736/introductory-note-for-jbcb-special-issue
#5
Chandra Verma, Peter Bond
No abstract text is available yet for this article.
December 30, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28152643/a-study-of-structural-properties-of-gene-network-graphs-for-mathematical-modeling-of-integrated-mosaic-gene-networks
#6
Olga V Petrovskaya, Evgeny D Petrovskiy, Inna N Lavrik, Vladimir A Ivanisenko
Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts...
December 22, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28150521/drug-repurposing-and-therapeutic-anti-microrna-predictions-for-inhibition-of-oxidized-low-density-lipoprotein-induced-vascular-smooth-muscle-cell-associated-diseases
#7
Shun-Tsung Chen, Chien-Hung Huang, Victor C Kok, Chi-Ying F Huang, Jin-Shuei Ciou, Jeffrey J P Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng
Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs...
December 22, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28052708/chaos-and-hyperchaos-in-simple-gene-network-with-negative-feedback-and-time-delays
#8
Tamara M Khlebodarova, Vladislav V Kogai, Stanislav I Fadeev, Vitaly A Likhoshvai
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos...
November 29, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27899048/the-method-for-breast-cancer-grade-prediction-and-pathway-analysis-based-on-improved-multiple-kernel-learning
#9
Tianci Song, Yan Wang, Wei Du, Sha Cao, Yuan Tian, Yanchun Liang
Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer grade can markedly elevate the detection of early breast cancer and efficiently guide its treatment. With the advent of high-throughput profiling technology, a large number of data of different types are rapidly generated, and each data provides its unique biological insight...
November 29, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28073302/is-the-average-shortest-path-length-of-gene-set-a-reflection-of-their-biological-relatedness
#10
Varsha Embar, Adam Handen, Madhavi K Ganapathiraju
When a set of genes are identified to be related to a disease, say through gene expression analysis, it is common to examine the average distance among their protein products in the human interactome as a measure of biological relatedness of these genes. The reasoning for this is that, genes associated with a disease would tend to be functionally related, and that functionally related genes would be closely connected to each other in the interactome. Typically, average shortest path length (ASPL) of disease genes (although referred to as genes in the context of disease-associations, the interactions are among protein-products of these genes) is compared to ASPL of randomly selected genes or to ASPL in a randomly permuted network...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28073301/author-index-volume-14-2016
#11
(no author information available yet)
No abstract text is available yet for this article.
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27774871/phrased-ml-a-paraphrased-human-readable-adaptation-of-sed-ml
#12
Kiri Choi, Lucian P Smith, J Kyle Medley, Herbert M Sauro
MOTIVATION: Model simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format. RESULTS: phraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27650662/global-peak-alignment-for-comprehensive-two-dimensional-gas-chromatography-mass-spectrometry-using-point-matching-algorithms
#13
Beichuan Deng, Seongho Kim, Hengguang Li, Elisabeth Heath, Xiang Zhang
Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC[Formula: see text][Formula: see text][Formula: see text]GC-MS) has been used to analyze multiple samples in a metabolomics study. However, due to some uncontrollable experimental conditions, such as the differences in temperature or pressure, matrix effects on samples and stationary phase degradation, there is always a shift of retention times in the two GC columns between samples. In order to correct the retention time shifts in GC[Formula: see text][Formula: see text][Formula: see text]GC-MS, the peak alignment is a crucial data analysis step to recognize the peaks generated by the same metabolite in different samples...
December 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28110603/development-of-software-and-modification-of-q-fish-protocol-for-estimation-of-individual-telomere-length-in-immunopathology
#14
M Sh Barkovskaya, A G Bogomolov, N Yu Knauer, N B Rubtsov, V A Kozlov
Telomere length is an important indicator of proliferative cell history and potential. Decreasing telomere length in the cells of an immune system can indicate immune aging in immune-mediated and chronic inflammatory diseases. Quantitative fluorescent in situ hybridization (Q-FISH) of a labeled (C3TA[Formula: see text] peptide nucleic acid probe onto fixed metaphase cells followed by digital image microscopy allows the evaluation of telomere length in the arms of individual chromosomes. Computer-assisted analysis of microscopic images can provide quantitative information on the number of telomeric repeats in individual telomeres...
November 24, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28033735/pass-based-approach-to-predict-hiv-1-reverse-transcriptase-resistance
#15
Olga Tarasova, Dmitry Filimonov, Vladimir Poroikov
HIV reverse transcriptase (RT) inhibitors targeting the early stages of virus-host interactions are of great interest to scientists. Acquired HIV RT resistance happens due to mutations in a particular region of the pol gene encoding the HIV RT amino acid sequence. We propose an application of the previously developed PASS algorithm for prediction of amino acid substitutions potentially involved in the resistance of HIV-1 based on open data. In our work, we used more than 3200 HIV-1 RT variants from the publicly available Stanford HIV RT and protease sequence database already tested for 10 anti-HIV drugs including both nucleoside and non-nucleoside RT inhibitors...
November 22, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27989220/mathematical-model-of-lsrr-binding-and-derepression-in-escherichia-coli-k12
#16
Steven M Graff, William E Bentley
Quorum sensing (QS) enables bacterial communication and collective behavior in response to self-secreted signaling molecules. Unlocking its genetic regulation will provide insight towards understanding its influence on pathogenesis, formation of biofilms, and many other phenotypes. There are few datasets available that link QS-mediated gene expression to its regulatory components and even fewer mathematical models that incorporate known mechanistic detail. By integrating these data with annotated sequence information, mathematical inferences can be pieced together that shed light on regulatory structure...
November 16, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28024450/age-estimation-for-the-genus-cymbidium-orchidaceae-epidendroideae-with-implementation-of-fossil-data-calibration-using-molecular-markers-its2-matk-and-phylogeographic-inference-from-ancestral-area-reconstruction
#17
Ruchishree Konhar, Manish Debnath, Jean Valrie Marbaniang, Devendra Kumar Biswal, Pramod Tandon
Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions...
November 9, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27908222/contribution-of-bacterial-promoter-elements-to-transcription-start-site-detection-accuracy
#18
Milos Nikolic, Tamara Stankovic, Marko Djordjevic
Accurately detecting transcription start sites (TSS) is a starting point for understanding gene transcription, and an important ingredient in a number of applications necessary for functional gene annotation, such as gene and operon predictions. Available methods for TSS detection in bacteria use very different description of the bacterial promoter structure and all of them show low accuracy. It is therefore unclear which promoter features should be included in TSS recognition, and how their accuracy impacts the search detection...
November 2, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27832721/identification-of-residues-of-the-archaeal-rna-binding-nip7-proteins-specific-to-environmental-conditions
#19
Kirill E Medvedev, Nikolay A Kolchanov, Dmitry A Afonnikov
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism's habitat. The number of such positions related to pressure change is much lower than related to temperature change...
October 14, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27696928/introduction-to-the-special-issue-on-giw-2016
#20
Shuigeng Zhou, Phoebe Yi-Ping Chen, Hiroshi Mamitsuka
No abstract text is available yet for this article.
October 3, 2016: Journal of Bioinformatics and Computational Biology
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